I really, really detest AA connections through PHL. I have been burned there on multiple in-country trips. That being said, my last three (forced - no viable alternate) connections through PHL have worked out unexpectedly well, and I may be forced to reconsider my objections to PHL. Depending on the gates and any personal mobility issues, I don't see a big problem with a 40-minute connection. I recently did a short connection between B and C gates, and it wasn't a problem. A and F gates, that may be a very different experience. Do some flight tracking on the aa.com website, or a site such as flightaware.com and see if you can get an idea where your flights typically arrive/depart from.

As to baggage, AA has improved their app by incorporating the old USAir bag tracking capabilities into the app. You can see from the app whether or not your bags have actually been loaded onto your aircraft. By that time it's already too late, so I always have at least one day of clothes and other necessities in my carry-on. Beyond one day, I've got plastic...